Chemical Level of Organization: Foundations for Anatomy & Physiology

Unit 2: Chemical Level of Organization

Introduction

Understanding the chemical basis of life is essential for studying anatomy and physiology. The human body is composed of atoms, molecules, and compounds that interact to form the structures and functions necessary for life. This unit covers the structure of atoms, chemical bonds, water, acids and bases, and the major classes of organic molecules.

Structure of an Atom

Subatomic Particles

• Atoms are the smallest units of matter that retain the properties of an element.

• Each atom consists of three main subatomic particles:

  • Protons: Positively charged particles located in the nucleus.

  • Neutrons: Neutral particles (no charge) also found in the nucleus.

  • Electrons (e-): Negatively charged particles orbiting the nucleus.

• Atoms are electrically neutral when the number of protons equals the number of electrons.

• Isotopes are atoms of the same element with different numbers of neutrons.

Ions

Formation and Importance

• An ion is an atom or molecule that has gained or lost one or more electrons, acquiring a net charge.

• Anion: An atom that gains electrons (negatively charged).

• Cation: An atom that loses electrons (positively charged).

• Electrolytes are ions in body fluids that conduct electricity and are vital for physiological functions.

Ion	Symbol	Role in Body
Calcium	Ca2+	Muscle contraction, nerve function, bone structure
Sodium	Na+	Fluid balance, nerve impulses
Potassium	K+	Nerve impulses, muscle contraction
Hydrogen	H+	pH regulation
Chloride	Cl-	Fluid balance, stomach acid

Chemical Bonds

Types of Bonds

• Chemical bonds hold atoms together to form molecules.

• Ionic Bonds: Formed by the transfer of electrons from one atom to another, resulting in oppositely charged ions that attract each other.

  • Example: Formation of NaCl (table salt):

    • Na loses an electron → Na+

    • Cl gains an electron → Cl-

    • Na+ and Cl- attract to form NaCl.

  • In water, NaCl dissociates into Na+ and Cl-.

• Covalent Bonds: Formed by the sharing of electrons between atoms.

  • Example: O2 (oxygen gas) is formed by two oxygen atoms sharing electrons.

Organic vs. Inorganic Compounds

• Organic substances: Contain covalently bonded carbon atoms (e.g., carbohydrates, proteins, lipids, nucleic acids).

• Inorganic substances: Usually lack carbon atoms (e.g., water, salts, O2), with exceptions such as H2CO3 (carbonic acid), HCO3- (bicarbonate), CO2 (carbon dioxide), and CO (carbon monoxide).

Water (Inorganic)

Properties and Functions

• Water (H2O) is the most abundant substance in cells.

• Composed of two hydrogen atoms and one oxygen atom.

• Polar molecule: Unequal sharing of electrons creates a slight charge difference across the molecule.

• Acts as a universal solvent, facilitating chemical reactions in the body.

• Transports chemicals (e.g., O2, nutrients) and helps maintain body temperature (~37°C).

Acids and Bases

Definitions and Importance

• Acids: Substances that dissociate in water to release H+ ions.

  • Increase [H+] → decrease pH (more acidic).

  • Example: Hydrochloric acid (HCl) in water: $\mathrm{HCl} \rightarrow \mathrm{H}^+ + \mathrm{Cl}^-$

• Bases: Substances that bind to (or buffer) free H+ ions in water.

  • Decrease [H+] → increase pH (more basic/alkaline).

  • Examples:

    • Sodium hydroxide (NaOH) in water: $\mathrm{NaOH} \rightarrow \mathrm{Na}^+ + \mathrm{OH}^-$

    • Bicarbonate buffering: $\mathrm{HCO}_3^- + \mathrm{H}^+ \rightarrow \mathrm{H}_2\mathrm{CO}_3 \rightarrow \mathrm{H}_2\mathrm{O} + \mathrm{CO}_2$

  • OH- and HCO3- act as bases by binding free H+ ions.

pH Scale

• The pH scale measures the concentration of free H+ ions in a solution.

• Scale ranges from 0 (most acidic) to 14 (most basic/alkaline), with 7 being neutral.

• Blood pH is tightly regulated between 7.35 and 7.45.

• Neutralization reaction: $\mathrm{OH}^- + \mathrm{H}^+ \rightarrow \mathrm{H}_2\mathrm{O}$

Important Organic Substances

1. Carbohydrates

• Composed of carbon (C), hydrogen (H), and oxygen (O); general formula: $(\mathrm{CH}_2\mathrm{O})_n$

• Functions:

  • Primary source of energy for cells (e.g., glucose: C6H12O6).

  • Structural components (e.g., in DNA and RNA).

• Types:

  • Monosaccharides: Simple sugars (e.g., glucose, fructose, ribose, deoxyribose).

  • Disaccharides: Two monosaccharides covalently bonded (e.g., glucose + fructose → sucrose).

  • Polysaccharides: Many monosaccharides bonded together (e.g., glycogen in animals, starch in plants).

2. Lipids

• Composed of C, H, and O (different ratio than carbohydrates).

• Examples: Fats, oils, waxes, fatty acids.

• Insoluble in water (nonpolar).

• Functions:

  • Protection (padding for organs).

  • Building cell membranes.

  • Energy storage.

• Types:

  • Glycerides: Most common lipid in body and diet; composed of glycerol and fatty acids.

    • Monoglyceride: Glycerol + 1 fatty acid

    • Diglyceride: Glycerol + 2 fatty acids

    • Triglyceride: Glycerol + 3 fatty acids

  • Phospholipids: Contain a phosphate "head" (polar, hydrophilic), glycerol backbone, and two fatty acid "tails" (nonpolar, hydrophobic). Major component of cell membranes.

  • Cholesterol: Found in cell membranes; precursor for steroid synthesis.

  • Steroids: Derived from cholesterol (e.g., bile salts, vitamin D, hormones like testosterone and estrogen).

3. Proteins

• Composed of C, H, O, N (sometimes S).

• Examples: Collagen, enzymes, antibodies.

• Functions:

  • Structural materials (e.g., collagen in connective tissue).

  • Enzymes, hormones, transporters.

  • Antibodies (immune defense).

  • Energy source (when carbohydrates and lipids are low).

• Levels of Organization:

  • Amino acids: Building blocks of proteins (e.g., glycine).

  • Dipeptides: Two amino acids joined together.

  • Polypeptides: Many amino acids linked in a chain.

  • Protein: One or more polypeptides folded into a functional shape.

4. Nucleic Acids

• Composed of C, H, O, N, P.

• Types:

  • DNA (deoxyribonucleic acid)

  • RNA (ribonucleic acid)

• Nucleotides are the building blocks, each containing:

  • Phosphate group (PO4-)

  • Monosaccharide (ribose in RNA, deoxyribose in DNA)

  • Organic base: Adenine (A), Thymine (T, DNA only), Uracil (U, RNA only), Cytosine (C), Guanine (G)

• DNA Structure:

  • Double-stranded helix (twisted ladder)

  • Bases pair: A-T, G-C

  • Alternating sugar and phosphate form the backbone; bases form the rungs

  • Functions: Cellular reproduction, template for RNA synthesis

• RNA Structure:

  • Single-stranded

  • Bases pair: A-U, G-C

  • Function: Protein synthesis

5. Adenosine Triphosphate (ATP)

• ATP is a modified RNA nucleotide that stores and provides energy for cellular activities.

• Structure: Adenosine (ribose + adenine) + three phosphate groups

• High-energy bonds (represented as "~") between phosphate groups store energy.

• When the terminal phosphate bond is broken, energy is released for immediate use: $\mathrm{ATP} \rightarrow \mathrm{ADP} + \mathrm{P}_i$